[gmx-users] Hydrogen bonding criteria in Gromacs

[Quyen V. Vu]

Hydrogen bonding is approximated by charge-dipole interaction, which is
very orientation-sensitive, the energy of this kind interactions
are proportional to the cosine of the angle.
https://en.wikibooks.org/wiki/Molecular_Simulation/Charge-Dipole_Interactions



On Wed, Jan 15, 2020 at 5:59 PM Pandya, Akash <akash.pandya.15 at ucl.ac.uk>
wrote:

> Hi all,
>
> I  wanted to ask a couple of questions about the hydrogen bonding
> calculation in Gromacs.
>
>
>   1.   Why is the default angle cutoff 30 degrees? The reason I ask this
> is because I’ve seen in other packages with higher angle cutoffs.
>   2.  What’s the best way to define cutoffs for my system? I know this is
> ambiguous, but is there a procedure I can use to decide?
>
> Any guidance will be much appreciated.
>
> Thank you,
>
> Akash
>
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